title: HC 496


title: HomTum3

status: Public on Nov 13 2019

type: SRA

city: Beijing

first: Yang

last: Liu

address: 30 Xueyuan Road, Haidian District

country: China

institute: University of Science and Technology Beijing

library_source: transcriptomic

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensemble_GRCm38.90 whole genome using tophat2  with parameters  -p 8 -N 2 --read-edit-dist 2
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. Then we used the DESeq2 R package (1.20.0) in R to analyze the differential expression of two conditions/groups (three biological replicates per condition).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 values for each Sample ...

molecule: polyA RNA

organism: Homo sapiens

source_name: Fibrosarcoma cells

extract_protocol:
A small number of HT1080 cells and fibroblast cells (20-50 cells) were manually retrieved from the schematic features by using a mouth pipette with a self-pulled capillary (tip open about 40 μm) after coculturing for 24h. Labeled with different kind of cell-tracker dyes, these two types of cells have been observed under a fluorescence microscope (AZ100, Nikon, Japan) to distinguish target cell types, and then transferred into PCR tubes from mouth pipet for cell lysis. cDNA were further purified by QIAquick PCR purification kit.0.5-5 kb fragments were excised from agarose gel electrophoresis and purified by QIAquick gel extraction kit. Then each sample was amplified by another 10 cycles of PCR using amine-blocked primers (95 °C for 3 min, then 10 cycles of 95 °C for 30 s, 67 °C for 1 min and 72 °C for 6min (+6 s each cycle) with a 4 °C and hold). After the second purification, products were used for sequencing library preparation.
Library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.

tag: tissue

value: connective tissue

tag: cell type

value: HT1080 (Homoculture)

tag: developmental stage

value: within 50 generations

tag: culture condition

value: single cultivation


title: HomTum1


title: HomTum2


title: HC 480

city: Ottawa

first: Ziying

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

description: wheat treated with F. graminearum inoculation 2days

data_processing:
RNA-seq reads were preprocessed by trimming the adaptor sequences, filtering low-quality reads (Phred Score <=20 [Phred]) and eliminating short reads (length <= 20 bps) using software package from Stanford University (http://sfg.stanford.edu/)
RAN-seq reads were aligned to the pan-genome of Chinese Spring (IWGSC RefSeq v1.0) from the IWGSC sequence repository hosted by URGI-INRA (https://wheat-urgi.versailles.inra.fr/) and Fusarium graminearum reference genome (Fusarium graminearum str. PH-1) from EnsemblFungi (http://fungi.ensembl.org/, Release 35) using STAR v2.5.3a
R package DESeq2 was used for data normalization and to generate differentially expressed gene (DEG)
Genome_build: IWGSC RefSeq v1.0; Fusarium graminearum str. PH-1
Supplementary_files_format_and_content: Raw read counts data

molecule: total RNA

organism: Triticum aestivum

source_name: whole head

growth_protocol: Eighty-five doubled haploid lines derived from the cross Wuhan-1/Nyubai and the two parents were grown in controlled-environment cabinets with 16h light at 20°C and 8h dark at 16°C until mid-anthesis.

extract_protocol:
Total RNA was extracted using the TRI-Reagent (Molecular Research Center Inc) following manufacturer’s instructions, except for the following modification: the aqueous phase separation was technically implemented with phase-lock gel tubes (5 PRIME Inc., Gaithersburg, MD, USA) before the isopropanol precipitation. Crude total RNAs were cleaned up using the RNeasy Mini Kit (Qiagen, Mississauga, Canada), including a DNase I treatment from RNase-free DNase set (Qiagen), according to manufacturer’s instructions. RNA integrity and quality were initially tested by separation on denaturing 1% formaldehyde agarose gel electrophoresis; quantification and additional quality evaluation were performed using the QIAxpert instrument (Qiagen, Missisauga, Canada). RNA was processed for deep paired-end RNA sequencing (RNA-seq) using Illumina HiSeq 2500
Libraries were prepared according to Illumina's instructions, using the TruSeq RNA v2 LT kit and sequenced on the Genome Analyzer following the manufacturer's protocols (https://www.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf).

treatment_protocol: Heads at mid-anthesis were point inoculated with 10 μL of a F. graminearum (strain DAOM233423, Collection of Fungal Cultures, Agriculture and Agri-Food Canada, Ottawa, Canada) macroconidial spore suspension at 1 x 105 spores/mL using a micropipette between the lemma and palea of two basal florets of each fully developed spikelet on each treated head. Following inoculation, plants were transferred into another growth chamber where they were misted overhead; pots were disposed in a random order. Misting was for two days, 30 sec every 1 h, during the light period. Inoculated heads were collected at 2 dpi and 5 to 6 whole heads were pooled into one sample per DH line.

tag: genotype

value: Wuhan x Nuybai

value: whole head

tag: treatment

value: F. graminearum

tag: sample taken (dpi)


title: HC 478


title: HC 484


title: HC 474


title: CoTum2

value: HT1080 (Coculture with NHDF)

value: coculture with NHDF 24h


title: HC 470-2


title: HC 493


title: HC 475


title: CoTum3


title: HC 490


title: CoFib1

source_name: Normal human dermal fibroblasts

value: derma

value: NHDF (Coculture with HT1080)

value: the fourth-tenth generation

value: coculture with HT1080 cells 24h


title: HC 470


title: CoTum1


title: HC 469


title: HC 472


title: HC 469-2


title: HC 468-2


title: HC 479


title: RNAseq SP ZT19 rep1

city: College Station

first: Christine

last: Merlin

state: TX

address: 3258 TAMU

department: Biology

country: USA

institute: Texas A&M University

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.38 and RTA 1.18.61 software with default parameter settings. Sequencer .bcl basecall files were formatted into .fastq files using CASAVA_v1.8.2 script configureBclToFastq.pl.
Reads were mapped to the monarch genome (assembly v3; Zhan and Reppert, 2013) using TopHat2 (Kim et al, 2013) with parameters “--read-realign-edit-dist 2 -g 1 --b2-sensitive”.
Expression levels of transcripts were quantified in each sample using Cufflinks (Trapnell et al, 2010; 2012).
RAIN (Thaben & Westermark, 2014) and MetaCycle (Wu et al., 2016) were used to identify cycling genes meeting the following criteria: (1) three or more reads per kilo base per million (RPKM) in at least one time point, (2) adjusted p-value from RAIN and meta2d of MetaCycle ≤ 0.05, and (3) amplitude (maximal/minimal experimental values) > 1.3.
Heat maps were produced using heatmap.2 in gplots package for R. Gene ontology and KEGG pathway enrichment analysis were performed using Metascape (metascape.org).
Genome_build: Monarch genome (assembly v3)
Supplementary_files_format_and_content: Output from cufflinks in generic FPKM Tracking Format saved as plain text files containing the estimated gene-level expression values.

organism: Danaus plexippus

source_name: RNAseq SP ZT19_brain

growth_protocol: Wild-caught fall migratory monarch butterflies (Migrant) were housed indoors in glassine envelopes in a Percival incubator under fall-like conditions with light:dark (LD) cycle set to prevailing light conditions (11 h:13 h LD, 0730–1830 Central Standard Time), a constant temperature of 21 °C, and 70% humidity. Meanwhile, laboratory-raised LP and SP monarchs were obtained from eggs layed on potted tropical milkweed plants (Asclepias curassavica) by fertilized wild-type monarch females, which were manually crossed with wild-type males. Both wild-type females and males were previously maintained in 15-hours light: 9-hours dark at 25°C. Eggs were transferred to petri dishes onto milkweed leaves and divided in two groups placed in Percival incubators respectively under 15-hours light: 9-hours dark (long photoperiod; LP) and under 10-hours light: 14-hours dark (short photoperiod; SP), both at constant temperature of 21°C and 70% humidity. Starting at the second instar, larvae were raised individually on semi-artificial diet until pupation. Post-eclosion, adult monarchs were housed in glassine envelopes and were manually fed a 25% honey solution daily until dissection.

extract_protocol:
Brains of wild-caught migrants and of monarchs raised indoors in LP and SP were dissected in 0.5X RNA later (Invitrogen) to prevent RNA degradation, the retinal pigmented photoreceptor layer was removed, and the brains were stored at -80oC until use. For each seasonal phenotype/photoperiodic condition, three pooled brains were collected in two replicates at ZT1, ZT4, ZT7, ZT10, ZT13, ZT16, ZT19, and ZT22. For each sample, total RNA was extracted using an RNeasy Mini kit (Qiagen).
For samples from wild-caught migrants, polyA+ RNA was isolated from 2 μg of total RNA with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), and multiplexed libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos (New England Biolabs) and amplified with 12 PCR cycles, following the manufacturer’s recommendations. For samples from monarchs raised in LP and SP, multiplexed libraries were prepared by the Texas A&M AgriLife Genomics and Bioinformatics Facility using polyA+ RNA isolated from 1 μg of total RNA, and multiplexed libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina), following the manufacturer’s recommendations. Libraries quality and size distribution was verified on a Bioanalyzer, libraries were quantified by real-time quantitative PCR, and 16 multiplexed libraries were mixed in equimolar ratios and sequenced on a Hi-seq 2500 (Illumina) using 50bp single end reads.

treatment_protocol: After capture and eclosion, migrants, LP and SP were entrained for a minimum of 7 days respectively in 11:13, 15:9, and 10:14 LD cycles at 21ºC.

value: wild-type

tag: Sex

value: male

value: 3 brains


title: HC 463


title: RNAseq SP ZT22 rep1

source_name: RNAseq SP ZT22_brain


title: RNAseq SP ZT19 rep2

value: female


title: RNAseq SP ZT22 rep2


title: HC 463-2


title: HC 462-2


title: meningioma [17-17]

city: Houston

first: Tiemo

middle: J

last: Klisch

state: Texas

address: 1250 Moursund Street, N1370.08

department: Department of Molecular and Human Genetics

institute: Baylor College of Medicine

description:
17-17
Primary tumor

data_processing:
Individual libraries within the samples were demultiplexed using CASAVA 1.8.2 (CASAVA, RRID:SCR_001802).
TopHat2 (RRID:SCR_013035) was used for read alignment.
FastQC (RRID:SCR_014583) and RSeQC (RRID:SCR_005275) were used for read and alignment quality assessment.
HTSeq (RRID:SCR_005514) was used for expression count.
The reads were aligned to GRCh37 Human reference genome and mapping to the human transcriptome according to UCSC gene annotations.
Genome_build: GRCh37
Supplementary_files_format_and_content: *_htseq.counts.txt: Tab-delimited text files include expression count values for each Sample.

source_name: meningioma, WHO I, Discovery

extract_protocol:
AllPrep DNA/RNA/Protein Mini Kit (Qiagen).
Illumina, using SOP from BCM-HGSC (https://www.hgsc.bcm.edu).

tag: cohort

value: Discovery

value: Meningioma

tag: pathology

value: WHO I

tag: gender

value: Female

tag: age

tag: wes

value: Y


title: HC 468

value: Wuhan x Nuybai

value: whole head


title: HC 460-2

value: F. graminearum


title: HC 467


title: HC 460


title: HC 462


title: HC 458-2


title: RNAseq SP ZT16 rep1

source_name: RNAseq SP ZT16_brain


title: RNAseq SP ZT16 rep2


title: HC 455


title: RNAseq SP ZT13 rep2

source_name: RNAseq SP ZT13_brain


title: HC 458


title: HC 454


title: RNAseq SP ZT13 rep1


title: HC 453


title: HC 444


title: meningioma [17-18]

description:
17-18
Primary tumor


title: HC 450


title: HC 447


title: RNAseq SP ZT10 rep2

source_name: RNAseq SP ZT10_brain


title: RNAseq SP ZT10 rep1


title: HC 443


title: HC 441


title: HC 442


title: RNAseq SP ZT07 rep1

source_name: RNAseq SP ZT07_brain


title: RNAseq SP ZT07 rep2


title: HC 440


title: meningioma [16-45]

description:
16-45
Primary tumor

source_name: meningioma, WHO II, Discovery

value: WHO II

value: Male


title: HC 437


title: HC 438


title: RNAseq SP ZT04 rep1

source_name: RNAseq SP ZT04_brain


title: HC 425


title: meningioma [16-31]

description:
16-31
Primary tumor


title: RNAseq SP ZT01 rep2

source_name: RNAseq SP ZT01_brain


title: HC 423


title: RNAseq SP ZT01 rep1


title: HC 421


title: meningioma [16-03]

description:
16-03
Primary tumor


title: HC 418


title: HC 417


title: RNAseq Migrant ZT22 rep2

source_name: RNAseq Migrant ZT22_brain


title: HC 411


title: HC 415


title: HC 409


title: RNAseq Migrant ZT22 rep1


title: HC 439


title: RNAseq Migrant ZT19 rep2

source_name: RNAseq Migrant ZT19_brain


title: RNAseq Migrant ZT19 rep1


title: meningioma [15-15]

description:
15-15
Primary tumor


title: HC 406


title: HC 405


title: meningioma [14-05]

description:
14-05
Primary tumor


title: HC 434


title: RNAseq Migrant ZT16 rep2

source_name: RNAseq Migrant ZT16_brain


title: meningioma [DCC48]

description:
DCC48
Primary tumor


title: HC 401


title: HC 404


title: HC 400


title: RNAseq Migrant ZT16 rep1


title: HC 397


title: HC 399


title: HC 395


title: RNAseq Migrant ZT13 rep2

source_name: RNAseq Migrant ZT13_brain


title: HC 392


title: HC 391


title: HC 407


title: RNAseq Migrant ZT13 rep1


title: meningioma [DCC45]

description:
DCC45
Primary tumor


title: HC 388


title: HC 389


title: HC 390


title: RNAseq Migrant ZT10 rep2

source_name: RNAseq Migrant ZT10_brain


title: RNAseq Migrant ZT10 rep1


title: HC 386

source_name: whole head


title: HC 385


title: HC 384-2


title: RNAseq Migrant ZT07 rep2

source_name: RNAseq Migrant ZT07_brain


title: HC 384


title: RNAseq Migrant ZT07 rep1


title: HC 382-2


title: meningioma [17-06]

description:
17-06
Primary tumor


title: HC 378-2


title: HC 378


title: RNAseq Migrant ZT04 rep1

source_name: RNAseq Migrant ZT04_brain


title: HC 376-2


title: meningioma [16-43]

description:
16-43
Primary tumor


title: HC 382


title: RNAseq Migrant ZT04 rep2


title: HC 376


title: HC 375


title: meningioma [16-38]

description:
16-38
Primary tumor


title: HC374


title: HC 373-2


title: HC 373


title: RNAseq Migrant ZT01 rep2

source_name: RNAseq Migrant ZT01_brain


title: RNAseq Migrant ZT01 rep1


title: meningioma [16-11]

description:
16-11
Primary tumor

source_name: meningioma, WHO I, Discovery


title: D4-OSKM-2ndMEFs overexpression Zscan4f3A J3

city: Shanghai

first: Zhouli

last: Cheng

address: Mingdao Building, 131 Dong’An Rd, Shanghai, China

institute: Key Laboratory of Medical Epigenetics and Metabolism, and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to M18(gencode) whole genome using hisat2-2.1.0 with default parameters
stringtie was used for quantification of gene expression
Genome_build: M18(gencode)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and TPM value.

organism: Mus musculus

source_name: mouse primary MEF cells

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary mouse embryonic fibroblast

tag: strain


title: RNAseq LP ZT22 rep1

source_name: RNAseq LP ZT22_brain


title: HC 371


title: RNAseq LP ZT22 rep2


title: D4-OSKM-2ndMEFs overexpression Zscan4f3A J2


title: D4-OSKM-2ndMEFs overexpression Zscan4f3A J1


title: RNAseq LP ZT19 rep1

source_name: RNAseq LP ZT19_brain


title: RNAseq LP ZT19 rep2


title: D4-OSKM-2ndMEFs overexpression Zscan4f E3

description: D4-OSKM-2ndMEFs overexpression Zscan4f


title: HC 372


title: D4-OSKM-2ndMEFs overexpression Zscan4f E1

description: D4-OSKM-2ndMEFs overexpression Zscan4f


title: RNAseq LP ZT16 rep2

source_name: RNAseq LP ZT16_brain


title: RNAseq LP ZT16 rep1


title: D4-OSKM-2ndMEFs D2


title: meningioma [14-08]

description:
14-08
Primary tumor


title: RNAseq LP ZT13 rep2

source_name: RNAseq LP ZT13_brain


title: HC 372-2


title: input DNA of IgG

library_source: genomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to M18(gencode) whole genome using bowtie2 with parameters: --end-to-end
peaks were called using Macs2
Genome_build: M18(gencode)
Supplementary_files_format_and_content: bigwig files were generated using bam2wig.py(RSeQC)

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: passages

value: primary

tag: chip antibody


title: meningioma [16-37]

description:
16-37
Primary tumor


title: IgG_ChIPSeq

value: IgG (Sigma-Aldrich, 401590)


title: RNAseq LP ZT13 rep1

value: wild-type


title: RNAseq LP ZT10 rep2

source_name: RNAseq LP ZT10_brain

value: male


title: RNAseq LP ZT10 rep1

value: 3 brains


title: Zscan4f-flag_ChIPSeq

value: Flag (Shanghai Genomics Technology, 4110-20)


title: ROSEN-8

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
Resulting fastq files were aligned to the mouse mm10 reference genome using the STAR aligner algorithm
BAM files were sorted and indexed using Samtools and quality control was performed using Picard
Transcript read counts were determined was performed using Salmon
Genome_build: mm10
Supplementary_files_format_and_content: Salmon quantified, upper-quartile normalized read-counts.

growth_protocol: Tumors were orthotopically injected in sygeneic hosts. Tumors were allowed to progress to a 5mm diameter and opon which mice were randomized to study arms.

extract_protocol:
RNA was extracted using Qiagen Rneasy kits. mRNA quality was assessed using the Agilent Bioanalyzer.
Libraries for mRNA-seq made using total RNA and the Illumina TruSeq mRNA sample preparation kit
Paired end (2x50bp) sequencing was performed on the Illumina HiSeq 2000/2500 sequencer at the UNC High Throughput Sequencing Facility

treatment_protocol: Antibody was delivered using 100ul volumes and injected intraperitoneally bi-weekly for the following: anti-CTLA4 (125 ug, bioxcel BE0164), anti-PD1 (10mg/kg, bioxcel BE0146).

tag: model

tag: class

value: unknown

tag: time

value: end

tag: therapy

value: no

value: tumor


title: ROSEN-15

tag: tissue


title: RNAseq LP ZT07 rep2

source_name: RNAseq LP ZT07_brain

tag: genotype


title: RNAseq LP ZT07 rep1

value: female


title: input DNA of Zscan4f-flag

tag: cell type


title: D4-OSKM-2ndMEFs D3


title: IPMN rep2

city: kyoto

first: Ru

last: chen

address: kawahara-cho 53, shogoin, sakyo-ku

country: Japan

institute: kyoto university

data_processing:
Basecalls performed using bcl2fastq v1.8.4
CAGE-seq reads were aligned to the mm9 genome assembly using BWA_HISAT2
5′-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample
These CTSSs were used for subsequent clustering analysis by RECLU pipeline (Ohmiya H, eta al. BMC Genomics. 2014 Apr 25)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include CTSS values for each Sample

source_name: pancreas

growth_protocol: Mouse pancreatic cancer model derived pancreatic cancer cells were cultured in typically uncoated plastic in RPMI-1640 medium (Nacalai, Japan) supplemented with 10% fetal bovine serum and 1% penicillin/strepmycin.

extract_protocol:
Cells were collected using trypsin and RNA was harvested using Nucleospin RNA plus kit (Takara, Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ptf1a-Cre; KrasG12D; Brg1f/f

value: pancreas cancer


title: IPMN rep1


title: PanIN rep2

value: Ptf1a-Cre; KrasG12D; p53f/+


title: D4-OSKM-2ndMEFs D1


title: ROSEN-11


title: D4-OSKM-2ndMEFs overexpression Zscan4f E2

description: D4-OSKM-2ndMEFs overexpression Zscan4f


title: ROSEN-4

value: resistant


title: RNAseq LP ZT04 rep2

source_name: RNAseq LP ZT04_brain


title: ROSEN-9


title: ROSEN-13


title: RNAseq LP ZT04 rep1


title: CP-911


title: meningioma [16-40]

description:
16-40
Primary tumor

value: Discovery

value: Meningioma

value: WHO I

value: Male


title: meningioma [17-16]

description:
17-16
Primary tumor

value: Female

value: Y


title: RNAseq LP ZT01 rep2

source_name: RNAseq LP ZT01_brain

value: wild-type

value: male

value: 3 brains


title: RNAseq SP ZT04 rep2

source_name: RNAseq SP ZT04_brain


title: CP-910

value: unknown

value: end


title: PanIN rep1


title: RNAseq LP ZT01 rep1


title: CP-902

value: No

value: tumor


title: ROSEN-7

value: no


title: CP-909


title: CP-908


title: CP-898


title: CP-900


title: CP-896


title: meningioma [16-36]

description:
16-36
Primary tumor


title: CP-899


title: CP-901


title: C3TAG-160056


title: C3TAG-158413


title: C3TAG-159450


title: CP-897


title: meningioma [15-11]

description:
15-11
Primary tumor


title: Abl B Bim3’UTRmut/mut biological Replicate 1

city: Innsbruck

first: Verena

last: Labi

address: Innrain 80-82

department: Developmental Immunology

country: Austria

institute: Medical University Innsbruck

data_processing:
Illumina CASAVA (v1.8.2)  software used for basecalling.
RNAseq reads had 3’ adaptors trimmed in two passes using (flexbar 2.5) with parameters: --adapter-relaxed --adapter-trim-end RIGHT –max-uncalled 0 –adapter-gap -3 –format i1.8 –pre-trim-phred 30 --min-read-length 12.
The resulting reads were collapsed with a custom script to remove PCR amplification biases and were consequently trimmed by 2 nt from both 5’ and 3’ ends to remove the random nucleotides ligated with the adaptors.
For mapping we used bwa (0.7.12-r1039) in local alignment mode allowing for up to 3 mismatches in the whole read (bwa aln -n 3 -l 100) retaining aligments with mapping quality at least 13.
Aligned reads that contained RNA T:C conversions were collected further using a custom python script and were used for all the downstream analyses. Coverage plots were generated using R and Bioconductor.
putative miR-17-92 perfect match binding sites were identified at the longest annotated 3'UTRs of protein-coding genes (Bioconductor TxDb.Mmusculus.UCSC.mm9.knownGene annotation) as long as the 3'UTR was at least 50nts long. Sites with coverage of at least 5 reads in at least one sample were used for differential coverage analysis using the DESeq2 Bioconductor package.
Genome_build: mm9; A reference based on mm9 was created that contained the corresponding Bim 3’UTR mutations (mm9_Bim_MUT). Reads that did not map to rRNA (NCBIM37.65 rRNA FASTA downloaded from BioMart) were consequently mapped to mm9 for the Bim 3'UTR wild type libraries and to mm9_Bim_MUT for the Bim 3'UTRmut libraries.
Supplementary_files_format_and_content: DESeq2 output

source_name: Abelson virus transformed B cell progenitors, E14.5 murine fetal liver derived

growth_protocol: Abelson-virus transformed B cell progenitors were cultured at 37°C in a humidified atmosphere containing 5% CO2 in the following B cell medium: DMEM (Sigma, WHMISDZB) supplemented with 10% (v/v) FBS (Gibco 10270-106), 2 mM L-glutamine (Sigma G7513), 10 mM Hepes (LONZA BE17-737E), 1 mM sodium pyruvate (Gibco 13360-039), 1 x non-essential amino acids (Gibco 11140-035), 100 U/ml penicillin and 100 μg/ml streptomycin (Sigma 0781) and 50 µM β-mercapto-ethanol (Sigma M3148).

extract_protocol:
Abelson-virus transformed B cell progenitors were labeled with 500 µM 4-thiouridine (Carbosynth 13957-31-8) for 5 hours and crosslinked at a wavelength of 365 nm with a total dose of 2000 µJ/cm2 (UV Stratalinker 2400). Crosslinked cell pellets were flash frozen in liquid nitrogen and stored at -80ºC. PAR-CLIP was performed as described in Hafner et al. 2010 Cell 141, 129–141 with the following modifications. Briefly, UV-irradiated cells were lysed in NP-40 lysis buffer (50 mM HEPES-KOH at pH 7.5, 150 mM KCl, 2 mM EDTA, 0.5% (v/v) NP40, 0.5 mM DTT, complete EDTA-free protease inhibitor cocktail). Freshly prepared lysates were incubated with protein G magnetic beads (Invitrogen 100-03D), pre-coupled to anti-mouse Ago2 antibody (Wako Chemicals 018-22021) for 1 hour at 4ºC. Beads were washed with IP wash buffer (50 mM HEPES-KOH, pH 7.5, 150 mM KCl, 0.05% (v/v) NP40, 0.5 mM DTT, complete EDTA-free protease inhibitor cocktail) and subjected to RNase T1 (Fermentas EN0541) treatment (10U/µl) for 10 minutes at 37ºC. Immunoprecipitations were washed in IP wash buffer and incubated with calf intestinal phosphatase (New England BioLabs M0290), followed by radioactive end-labeling using T4 polynucleotide kinase (New England BioLabs M0201). The crosslinked protein-RNA complexes were resolved on a 4-12% NuPAGE gel (Invitrogen WG1402BOX). The SDS-PAGE gel was transferred to a nitrocellulose membrane and the protein-RNA complex migrating at the expected molecular weight was excised. RNA was isolated by Proteinase K (Roche 03115801001) treatment and phenol-chloroform extraction.
Sequencing libraries were constructed as described in Hafner et al. 2010 Cell 141, 129–141.

treatment_protocol: Generation of Abelson-virus transformed B cell progenitors: Single cell suspensions of E14.5 fetal livers were prepared in buffer ((phosphate buffered saline (PBS) with 3% (v/v) fetal calf serum (FCS) (Gibco 10270-106, Lot: 41Q7415K or 42G9363K))) by gentle homogenization through 70 µM nylon mesh filters (Falcon 352350). Abelson virus was prepared by CaCl2 precipitation. The pMSCV-v-Abl retroviral vector coding for the Abelson kinase was generated from the pMIG-120 retroviral vector by removing a 1.3kb fragment containing the IRES and GFP cDNA. Briefly, PlatE packaging cells were grown to a density of 80% in B cell medium, and 25 μM chloroquine (SIGMA C6628) was added shortly before precipitation.62 μl of 2 M CaCl2 was added dropwise to 438 μl of viral DNA (100 μg of pMSCV-v-Abl), and subsequently 500 μl 2 x HBS (280 mM NaCl, 50 mM HEPES, 1.5 mM Na2HPO4, 12 mM Dextrose, 10 mM KCl; adjust pH to 7.08 with 0.5 N NaOH) was added dropwise to the DNA solution to form a precipitate. After 15 minutes, the precipitate was added dropwise to the PlatE cells. After 14 hours incubation at 37°C, the medium was changed. 24 hours later, viral supernatant was harvested, filtered with a 0.45 μm filter (Sartorius Minisart 16537) and freshly used. 1 x 106 fetal liver cells were plated in 2 ml fresh viral supernatant/6-well. Before, each 6-well was coated with 50 μg/ml Retronectin (TAKARA T100A) in PBS o/n at 4°C, subsequently blocked with 2% BSA in PBS for 1 hour at room temperature, washed twice with PBS and loaded with 2 ml of fresh viral supernatant for 1 hour at 37°C. After discarding the viral supernatant, cells were resuspended in 1 ml of fresh viral supernatant including 6 μg/ml polybrene and 1 ml B cell medium supplemented with 10 ng/ml IL-7 (Peprotech 217-17) to support transformation. Fetal liver cells were spin-infected in 6-well plates at 3000 rpm at 30°C for 2 hours, filled up to 4 ml with B cell medium and incubated o/n at 37°C. Two-third of the B cell medium was exchanged every other day for 8 days. Then, cell pools were transferred into culture flasks and expanded in B cell medium without IL-7. For each biological replicate 2*10^8 cells were used.

tag: embryonic developmental stage

tag: genetic background


title: Abl B wild type Replicate biological 2

value: wild type


title: Abl B wild type biological Replicate 1


title: Abl B Bim3’UTRmut/mut biological Replicate 2


title: meningioma [DCC3]

description:
DCC3
Primary tumor

tag: cohort


title: WT_2

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
alignment TopHat v2.0.6
featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited gene raw counts

growth_protocol: Mice were aged to 9 months of age and euthanized for RNA extraction and cDNA library preparation

extract_protocol:
Total brain (cortex) RNA extracts were purified according to manufacturer’s instruction using the Qiagen Qiazol Lysis Reagent (Cat# 79306) and RNeasy Mini kit (Cat# 73404).
Paired-end sequencing libraries were prepared by the Mayo Clinic sequencing core facilities (Rochester, MN) with the TruSeq Stranded Total Sample Preparation kit (Illumina), after which samples were subjected to quality control, cluster generation, and sequencing at a read depth of 60 million reads per sample on the Illumina HiSeq 2000 platform.

tag: genotype/variation

value: wildtype

value: 9 months

tag: brain

value: brain


title: meningioma [DCC2]

description:
DCC2
Primary tumor

value: Discovery

value: Meningioma

tag: pathology

tag: gender

tag: age


title: WT_1


title: TIA1_het_2

value: P301S and TIA1 heterogeneous mouse


title: Tested sample 8

type: RNA

city: Baltimore

first: Ling

last: He

state: MD

address: 600 North Wolfe St

department: Department of Pediatrics-Division of Endocrinology

institute: The Johns Hopkins University School of Medicine

description: L-a1/2 KO-6

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Affymetrix CEL files were extracted with the Partek GS 6.6 platform and their data RMA and quantile-normalized to create log2 transcript signal values, which were used in subsequent ANOVA analysis.    Transcript annotation was subsequently updated.

label: biotin

source_name: Liver tissue of mice (16h fasting)

label_protocol: RNA was labeled with the Affymetrix GeneChip WT PLUS Reagent Kit using the manufacturer's protocol.

growth_protocol: 6 weeks old double floxed homozygous AMPK alpha 1 and alpha2 mice were fed on high-fat diet (60 % caloris) for 4 weeks. After the viral injection, mice were treated with metformin (50 mg/kg/day) for another three weeks before the termination of experiment.

extract_protocol: RNA was purified by using Trizol, followed by Qiagen Rneasy kit.

treatment_protocol: 10 weeks double floxed homozygous AMPK alpha 1 and alpha2 mice were injected with AAV8-TBG-empty vector or AAV8-TBG-Cre (1x10^11 GC/mouse) through jugular vein, and then, treated with metformin (50 mg/kg/day) for another 3 weeks.

value: liver

tag: background strain

value: 4 months

tag: Sex

tag: treatment

value: metaformin AMPK Cre KO

tag: genoype

value: TGB_Cre KO


title: Tested sample 6

description: L-a1/2 KO-6

value: male


title: Tested sample 5

description: L-a1/2 KO-5


title: Tested sample 2

description: L-a1/2 KO-2


title: Tested sample 4

description: L-a1/2 KO-4


title: Tested sample 7

description: L-a1/2 KO-5


title: P301S-TIA1_het_3

value: TIA1 heterogeneous mouse


title: Tested sample 1

description: L-a1/2 KO-1


title: P301S-TIA1_het_2


title: Control replicate 5

description: Floxed a1/2-5

value: metaformin control

value: TGB_empty-vector WT


title: Control replicate 6

description: Floxed a1/2-6


title: TIA1_het_3


title: Tested sample 3

description: L-a1/2 KO-3


title: Control replicate 4

description: Floxed a1/2-4


title: P301S_2

value: P301S mouse


title: P301S_3


title: Control replicate 3

description: Floxed a1/2-3


title: P301S_1


title: TIA1_het_1


title: Control replicate 1

description: Floxed a1/2-1


title: HC 413

source_name: whole head

value: Wuhan x Nuybai

value: whole head

value: F. graminearum

tag: sample taken (dpi)


title: HC 422


title: Abl B Bim3’UTRmut/mut 7

description:
miRNA
SAMPLE 7

hyb_protocol: NanoString Technologies GXA-MMIR15-12; See manufacturer instructions at https://www.nanostring.com/products/mirna-assays/mirna-panels

data_processing: none - raw data were used for analysis

label_protocol: Continuous sample labeling

growth_protocol: Abl B cells were cultured at 37°C in a humidified atmosphere containing 5% CO2 in the following B cell medium: DMEM (Sigma, WHMISDZB) supplemented with 10% (v/v) FBS (Gibco 10270-106), 2 mM L-glutamine (Sigma G7513), 10 mM Hepes (LONZA BE17-737E), 1 mM sodium pyruvate (Gibco 13360-039), 1 x non-essential amino acids (Gibco 11140-035), 100 U/ml penicillin and 100 μg/ml streptomycin (Sigma 0781) and 50 µM β-mercapto-ethanol (Sigma M3148).

extract_protocol: Total RNA was extracted from in vitro cultivated Abl B cells using the miRNeasy mini kit (QIAGEN 217004). The concentration and purity of RNA was assessed using a NanoDrop spectrophotometer (Thermo Scientific). Samples with A260/280 ratios <2.0 and A260/230 ratios <1.5 were excluded from analysis. 100 ng of total RNA per sample was used as input for nCounter gene expression analysis (NanoString Technologies).

treatment_protocol: Generation of Abl B cell lines: Single cell suspensions of E14.5 fetal livers were prepared in buffer ((phosphate buffered saline (PBS) with 3% (v/v) fetal calf serum (FCS) (Gibco 10270-106, Lot: 41Q7415K or 42G9363K))) by gentle homogenization through 70 µM nylon mesh filters (Falcon 352350). Abelson virus was prepared by CaCl2 precipitation. The pMSCV-v-Abl retroviral vector coding for the Abelson kinase was generated from the pMIG-120 retroviral vector by removing a 1.3kb fragment containing the IRES and GFP cDNA. Briefly, PlatE packaging cells were grown to a density of 80% in B cell medium, and 25 μM chloroquine (SIGMA C6628) was added shortly before precipitation.62 μl of 2 M CaCl2 was added dropwise to 438 μl of viral DNA (100 μg of pMSCV-v-Abl), and subsequently 500 μl 2 x HBS (280 mM NaCl, 50 mM HEPES, 1.5 mM Na2HPO4, 12 mM Dextrose, 10 mM KCl; adjust pH to 7.08 with 0.5 N NaOH) was added dropwise to the DNA solution to form a precipitate. After 15 minutes, the precipitate was added dropwise to the PlatE cells. After 14 hours incubation at 37°C, the medium was changed. 24 hours later, viral supernatant was harvested, filtered with a 0.45 μm filter (Sartorius Minisart 16537) and freshly used.1 x 106 fetal liver cells were plated in 2 ml fresh viral supernatant/6-well. Before, each 6-well was coated with 50 μg/ml Retronectin (TAKARA T100A) in PBS o/n at 4°C, subsequently blocked with 2% BSA in PBS for 1 hour at room temperature, washed twice with PBS and loaded with 2 ml of fresh viral supernatant for 1 hour at 37°C. After discarding the viral supernatant, cells were resuspended in 1 ml of fresh viral supernatant including 6 μg/ml polybrene and 1 ml B cell medium supplemented with 10 ng/ml IL-7 (Peprotech 217-17) to support transformation. Fetal liver cells were spin-infected in 6-well plates at 3000 rpm at 30°C for 2 hours, filled up to 4 ml with B cell medium and incubated o/n at 37°C. Two-third of the B cell medium was exchanged every other day for 8 days. Then, cell pools were transferred into culture flasks and expanded in B cell medium without IL-7 until sufficient cell material for NanoString analysis was generated.

tag: developmental stage

value: embryo

tag: strain (genetic background)

value: Abelson virus transformed B cell progenitors


title: Abl B Bim3’UTRmut/mut 8

description:
miRNA
SAMPLE 8

scan_protocol: NanoString Technologies GXA-MMIR15-12; See manufacturer instructions at https://www.nanostring.com/products/mirna-assays/mirna-panels

tag: genotype

tag: tissue


title: Abl B Bim3’UTRmut/mut 9

description:
miRNA
SAMPLE 9

tag: cell type


title: WT_3

value: wildtype

value: 9 months

value: brain


title: Control replicate 2

description: Floxed a1/2-2

value: liver


title: Abl B wild type 5

description:
miRNA
SAMPLE 5

value: wild type


title: Abl B wild type 4

description:
miRNA
SAMPLE 4


title: HDAC9 knocked-out SK-UT-1 cells repA, clone D43

city: udine

first: raffaella

last: picco

address: piazzale kolbe 4

department: department of medical and biological sciences

country: Italy

institute: university of Udine

description:
replicate A
I

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were vst transformed and normalized using quantile normalization with the Lumi package in R.

source_name: SK-UT-1  Leiomyosarcomas cells HDAC9-/-, clone D43

label_protocol: Aliquots of RNAs were amplified and labelled according to the specifications of the Illumina® TotalPrep™ RNA Amplification Kit (Ambion, Austin,TX).

growth_protocol: SK-UT-1 cells were grown in DMEM (Euroclone) supplemented with 10%FBS, L-glutamine (2mM), penicillin (100U/ml) and streptomycin (100μg/ml) (Lonza) at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy columns (QIAGEN, Hilden, Germany)

treatment_protocol: CRISPR/Cas9 technology was applied to obtain HDAC4-/- clones and HDAC9-/- clones. The KO clones were screened by PCR, immunoblot and validated by Sanger sequencing.

tag: cell line


title: TRAF3KO 2

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were extracted with Illumina BeadStudio v3.2.3 and quantile normalized.

source_name: Mouse spleen

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: TRAF3-/- premalignant splenic B cells


title: TRAF3KO 3


title: HDAC9 knocked-out SK-UT-1 cells repB, clone 167

description:
replicate B
H

source_name: SK-UT-1  Leiomyosarcomas cells HDAC9-/-, clone 167


title: HDAC9 knocked-out SK-UT-1 cells repB, clone D43

description:
replicate B
L


title: HDAC9 knocked-out SK-UT-1 cells repA, clone 167

description:
replicate A
G


title: HDAC4 knocked-out SK-UT-1 cells repA, clone 125

description:
replicate A
E

source_name: SK-UT-1  Leiomyosarcomas cells HDAC4-/-, clone 125


title: HDAC4 knocked-out SK-UT-1 cells repB, clone 26

description:
replicate B
D

source_name: SK-UT-1  Leiomyosarcomas cells HDAC4-/-, clone 26


title: AD pt6 nonlesional

city: Saint Louis

first: Ting-Lin

last: Yang

state: Missouri

address: 660 S. Euclid Ave., CB 8123

institute: Washington University of St Louis

data_processing:
Sequences were aligned with STAR v2.0.4b
Gene counts were determined with Subread:featureCount v1.4.5
Transcript abundance was determined with Sailfish v0.6.3
Sequence performace was assessed with RSeQC v2.3
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files are the counts tables from Subread:featureCount for each sample as a text file, as well as a compiled csv file of RPKMs for each sample

source_name: skin

extract_protocol:
Skin punch biopsies were performed from lesional and nonlesional skin of atopic dermatitis patients; skin samples were placed in RNA Later and tissue was lysed using a bead homogenizer and RNA was isolated using the RNeasy mini kit (QIAGEN)
Libraries were constructed using the CloneTech SMARTer cDNA amplification kit with 10 ng of total RNA.

value: skin

tag: type

value: nonlesional

tag: disease state

value: atopic dermatitis


title: HDAC4 knocked-out SK-UT-1 cells repB, clone 125

description:
replicate B
F


title: AD pt6 lesional

value: lesional


title: Abl B Bim3’UTRmut/mut 6

description:
miRNA
SAMPLE 6


title: Abl B wild type 3

description:
miRNA
SAMPLE 3


title: Abl B wild type 1

description:
miRNA
SAMPLE 1


title: HDAC4 knocked-out SK-UT-1 cells repA, clone 26

description:
replicate A
C


title: TRAF3KO 1


title: AD pt5 lesional


title: AD pt4 nonlesional


title: Control 3

value: Normal splenic B cells


title: Control 1


title: Control 2


title: SK-UT-1 cells control repA

description:
replicate A
A

source_name: SK-UT-1  Leiomyosarcomas cells


title: HSC_CB_1

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

country: Germany

institute: Hannover Medical School

description: CD45+/CD34+/CD38-/CD45RA-/CD90high/CD49fhigh cord blood hematopoietic stem cells

data_processing:
Primary data analysis, including base calling and quality scoring is performed by real-time analysis or RTA (Version 2.4.11) on the sequencing instrument (NextSeq550). RTA performs image analysis and base calling during the sequencing run.
Raw data was processed by converting the BCL files into FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina)
The FASTQ files were adapted and quality trimmed using Trim Galore! (Version 0.4.1)
FASTQ files were mapped against a the human reference genome hg19 using STAR (version 2.5.0c) . BAM files were built in a 2-pass mapping (--twopassMode Basic) and were finally sorted (--outSAMtype BAM SortedByCoordinate).
Read counting was performed by featureCounts as part of the Subread (Liao et al.) software package (version 1.6.1) using gencode.v28lift37
Genome_build: hg19
Supplementary_files_format_and_content: text file with hgnc symbols and  raw counts for each gene

source_name: Cord Blood HSCs

extract_protocol:
Total RNA was isolated using RNeasy Micro Kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer. Ribosomal RNA was removed using NEBNext rRNA Depletion Kit.
5 ng total RNA was used for library preparation with the ‘SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian’ (Takara). Libraries were barcoded by a dual indexing approach and were amplified by 11 PCR cycles. Fragment length distribution was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (Agilent). Quantification was performed with the ‘Qubit® dsDNA HS Assay Kit’ (ThermoFisher). The combined library pools were denatured with sodium hydroxide and were finally diluted to 1.5 pM according to the Denature and Dilute Libraries Guide (Document # 15048776 v02; Illumina, San Diego, USA). 1.3 mL of each denatured pool was loaded on an Illumina NextSeq 550 sequencer using a High Output Flowcell for 75 bp single reads (#FC-404-2005; Illumina).

tag: facs


title: HSC_CB_3


title: AD pt5 nonlesional


title: SK-UT-1 cells control repB

description:
replicate B
B


title: 5A-2

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

country: Taiwan

institute: National Taiwan University

description:
SAMPLE 5
replicate 2

hyb_protocol: Standard Illumina HT-12 beadchips hybridization protocol

scan_protocol: Illumina HiScan standard scanning protocol

data_processing: The raw intensity values were background corrected by RMA, normalized by quantile normalization and then transformed into log2 scale in R

label_protocol: Standard Illumina HT-12 beadchips label protocol

growth_protocol: Cells were seeded at the denity of 9x10^5 per10-cm dish.

extract_protocol: RNA was extracted with Trizol reagent. The cDNA was synthesized from total RNA primed with T7 Oligo(dT) and amplified by an Illumina TotalPre RNA Amplification Kit (Ambion, Austin, USA).

treatment_protocol: SEMA5A was transfected into the cells 24 after seeding.

value: lung epithelial carcinoma cells

value: transfection of SEMA5A


title: 5A-3

description:
SAMPLE 6
replicate 3


title: AD pt3 nonlesional


title: AD pt3 lesional


title: baba3

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: baba treatment replicate 3

data_processing:
Lifescope v2.5.1 whole transcriptome pipeline.
Mapping versus Solanum lycopersicum SL2.40 build
Splice junction indexation with ITAG2.3 gene model
Table count generation within Lifescope WT pipeline with ITAG2.3 gene model
Genome_build: SL2.40
Supplementary_files_format_and_content: Lifescope whole transcriptome pipeline GENES table count (count+rpkm values)

organism: Solanum lycopersicum

source_name: plant leaves

growth_protocol: controlled conditions (16 h light, 1500 μmol m-2 s-1, 24 °C), 1L pots with nutrition twice a week (Hoagland solution)

extract_protocol:
TRIzol according to the manufacturer instructions. Ethanol precipitated RNA
PolyA+ RNAs were selected from 6µg total RNA with Dynabeads mRNA purificationkit (invitrogen). RNA were  fragmented 10 min at 95°C in RNAseIII buffer (Invitrogen) then adapter-ligated, reverse transcribed and amplified (5 cycles) with the reagents from the NEBNext Small RNA Library Prep Set for SOLiD. Amplified libraries were purified on Purelink PCR micro kit (Invitrogen) then subjected to additional PCR rounds (7 cycles) with primers from the 5500 W Conversion Primers Kit (Life Technologies). After Agencourt® AMPure® XP beads purification (Beckman Coulter), libraries were size-selected from 200 nt to 300 nt with the LabChip XT DNA 300 Assay Kit (Caliper Lifesciences). Libraries were finally converted with the enzyme kit from the 5500 W Conversion Primers Kit (Life Technologies), quantified with the Bioanalyzer High Sensitivity DNA Kit (Agilent) and sequenced on SOLiD 5500XL (Life Technologies) with single-end 50b reads.

treatment_protocol: spraying with the "hanging drop" method

value: leaflets

value: 5 weeks old plants

tag: cultivar

value: Marmande


title: HSPC_P2d4_2

description: day11 CD45+/CD34+/CD38-/CD45RA-/CD90high/CD49fhigh SLGE-hematopoietic progenitors

source_name: Phase 2 day 4 (total day 11) SLGE-HPC


title: ROSEN-6

tag: model

tag: class

value: unknown

tag: time

value: end

tag: therapy

value: no

value: tumor


title: AD pt2 nonlesional


title: GW20_Hippocampus-01

first: Suijuan

last: Zhong

state: Haidian

address: No.19 Xinjiekouwai Street

institute: Beijing Normal University

description: Sample 7

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to hg19 human genome by Cellranger(v2.0.1)
Filtered count matrix was merged by Seurat R Package(v2.1.0)
Genome_build: hg19
Supplementary_files_format_and_content: Filtered count matrix was formatted by mtx, and barcode and gene information was with tsv format

source_name: human embryonic hippocampus

extract_protocol:
Fetal retina tissue samples were collected in ice-cold artificial cerebrospinal fluid (ACSF)
Chromium™ Single Cell 3’ Reagent Kits v2，sample1(indexC6),sample2(indexB5),sample3(indexA3),sample4(indexA1),sample5(indexA2),sample6(indexD1)

tag: gestational week

value: hippocampus


title: GW20_Hippocampus-02

description: Sample 8


title: baba1

description: baba treatment replicate 1


title: AD pt4 lesional


title: HSPC_P2d4_3


title: AD pt2 lesional


title: water3

description: water treatment replicate 3


title: HEP_P1d7_3

description: day 7 human SLGE-hemato-endothelial progenitors, 6 days after Dox-induction of SLGE

source_name: Phase 1 day 7 SLGE-HEP Dox-induced


title: C-2

description:
SAMPLE 2
replicate 2

tag: treatment

value: control


title: C-1

description:
SAMPLE 1
replicate 1


title: HEP_P1d7_2


title: C-3

description:
SAMPLE 3
replicate 3


title: 5A-1

description:
SAMPLE 4
replicate 1


title: ATAC-HP2

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to hg19 human genome by STAR
Genome_build: hg19
Supplementary_files_format_and_content: bw

extract_protocol: Fetal retina tissue samples were collected in ice-cold artificial cerebrospinal fluid (ACSF)


title: AD pt1 lesional


title: ATAC-HP3


title: baba2

description: baba treatment replicate 2


title: water1

description: water treatment replicate 1


title: ATAC-HP1


title: HSPC_P2d4_1


title: LT3

city: Taigu

first: Chunlei

last: Zou

address: No.1 Mingxian Road

institute: Shanxi Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly.
The mapped reads of each sample were assembled by StringTie (v1.3.1) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.
CNCI (Coding-Non-Coding-Index) (v2) profiles adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations
Phast (v1.3) is a software package containing much of statistical programs, mostly used in phylogenetic, and phastCons is a conservation scoring and identificating program of conserved elements.
Genome_build: https://www.ncbi.nlm.nih.gov/genome/?term=Beta+vulgaris+L ; The file  transcript_annotation_and_coordinates.xlsx includes the annotation and/or coordinates for all analyzed known and novel transcripts.
Supplementary_files_format_and_content: text file with FPKM

organism: Beta vulgaris

source_name: 7 days alkaline treatment

growth_protocol: Pelleted seeds of sugar beet cultivar “KWS0143”, supplied by KWS company, Germany, were germinated in vermiculite with distilled water for a week, then irrigated with Hoagland solution for 3 weeks and finally transplanted to hydroponic device filled with Hoagland solution at 65% relative humidity, 25℃/20℃ (day/night), 450 μmol·m-2·s-1 light intensity and a photoperiod of 16 h light/8 h dark.

extract_protocol:
Total RNA was extracted using the Qiagen RNAeasy kit (Qiagen China, Shanghai, China) according to the manufacturer’s instructions. RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: After one more week, seedlings were treated with Hoagland solution, containing 75 mM mixed alkaline solution (Na2CO3:NaHCO3, 1:2) for 0 day (control, designated as C), 3 days (short-term treatment, designated as ST) and 7 days (long-term treatment, designated as LT).

value: Fresh leaves

value: Seedling stage

tag: age

value: 5 weeks


title: P1_d2_3

description: day 2 human SLGE-hemato-endothelial progenitors, 24 hrs after Dox-induction of SLGE

source_name: Phase 1 day 2 SLGE-HEP Dox-induced


title: LT2

tag: developmental stage


title: HeLa_CCL2_scRNAseq_3

city: Beijing

first: Xin

last: Zhang

state: Beijing

address: No.5 Yiheyuan Road

department: School of Life Sciences, BIOPIC

institute: Peking University

data_processing:
UMI counting
mapping using HISAT2 basic parameters
htseq counting the transcripts number
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files generated by htseq

source_name: HeLa CCL2 cell line

extract_protocol:
SMART-Seq2
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HeLa CCL2

tag: generation


title: D-glucose RNAseq 4

city: Berkeley

first: Samuel

middle: Thomas

last: Coradetti

state: CA

address: 1165 Glen Ave Apt B

department: Bioengineering

institute: UC Berkeley

data_processing:
Basecalls performed with CASAVA bcl2fastq_v2.17
Reads aligned to reference transcripts with hisat2-2.1.0
FPKM calculated with stringtie-1.3.3b
Genome_build: Joint Genome Institute R. toruloides version 4 (https://genome.jgi.doe.gov/Rhoto_IFO0880_4/Rhoto_IFO0880_4.home.html)
Supplementary_files_format_and_content: Tab-delimited abundances files from stringtie, FPKM

organism: Rhodotorula toruloides

source_name: Whole cells

growth_protocol: Liquid culture in Yeast Nitrogen Base plus carbon sources

extract_protocol:
Ribopure yeast RNA extraction kit
mRNA selection with dynabeads, TruSeq library construction protocol

treatment_protocol: Cells sampled in log phase.

tag: strain

tag: growth culture

value: D-glucose


title: D-glucose RNAseq 3


title: AD pt1 nonlesional

tag: tissue

value: skin

value: nonlesional

value: atopic dermatitis


title: P1_d2_1


title: Abl B wild type 2

description:
miRNA
SAMPLE 2

source_name: Abelson virus transformed B cell progenitors, E14.5 murine fetal liver derived

value: embryo

tag: strain (genetic background)

tag: genotype

value: wild type

value: liver

tag: cell type


title: HeLa_CCL2_scRNAseq_1

tag: cell line


title: Glycerol RNAseq 2

value: Glycerol


title: P1_d1_3

description: day 1 human SLGE-hemato-endothelial progenitors, after mesodermal priming

source_name: Phase 1 day 1 SLGE-HEP uninduced

tag: facs


title: GW27_Hippocampus

description: Sample 6


title: HeLa_CCL2_scRNAseq_2


title: Glycerol RNAseq 1


title: P1_d1_2


title: ST3

source_name: 3 days alkaline treatment

tag: cultivar


title: LT1


title: D-glucose RNAseq 2


title: ST1


title: GW25_Hippocampus

description: Sample 5


title: P1_d2_2


title: P1_d1_1


title: D-glucose RNAseq 1


title: GW22_Hippocampus-02

description: Sample 4


title: C3

source_name: control


title: iPS_3

description: human SLGE-transduced iPS

source_name: human iPS parental cell line


title: HEP_P1d7_1


title: GW22_Hippocampus-01

description: Sample 3


title: D-galacturonic acid RNAseq 3

value: D-galacturonic acid


title: C2


title: iPS_2

description: human SLGE-transduced iPS


title: GW18_Hippocampus

description: Sample 2


title: D-galacturonic acid RNAseq 2


title: C1


title: GW16_Hippocampus

description: Sample 1


title: water2

description: water treatment replicate 2

value: leaflets

value: 5 weeks old plants

value: Marmande


title: D-galacturonic acid RNAseq 1


title: ST2


title: iPS_1

description: human SLGE-transduced iPS


title: CIITA-null, Donor 1, Clone 5 [CIITA_Donor1_Rep1]

status: Public on Nov 12 2019

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The first 6 nucleotides and the last nucleotides at the point where the Phred score of an examined base fell below 20 were trimmed using in-house scripts.  If, after trimming, the read was shorter than 45-bp, the whole read was discarded.
Trimmed reads were mapped to the human reference genome (hg19) with a known transcriptome index (UCSC Known Gene annotation) with Tophat v2.1.1 using the very-sensitive preset, first strand library type, and providing the corresponding gene model annotation. Only the reads that mapped to a single unique location within the genome, with a maximum of two mismatches in the anchor region of the spliced alignment, were reported in these results. We used the default settings for all other Tophat options.
Tophat alignments were then processed by Cuffdiff (Cufflinks v2.2.1) to obtain differential gene expression using first strand library type, providing gene model annotation and the genome sequence file for detection and correction of sequence-specific bias that random hexamer can cause during library preparation.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKMs, fold changes, and p-values for each condition. Cuffdiff output format.

source_name: CRISPR/Cas9 CIITA targeted Human cord-blood endothelial cells

growth_protocol: Endothelial cells were isolated from placental cord-blood and grown in EGM2MV media, transduced with Cas9 and guide strands directed towards AAVS1, B2-Microglobulin, CIITA or B2M+CIITA, sorted by FACS for negative class I and II MHC expression and treated with 50 ng/mL human interferon gamma for 72 hours

extract_protocol:
RNA was extracted with Qiagen Rneasy kit with DNase treatment
Poly-A, strand-specific RNA library construction was performed by the Yale Center for Genomic Analysis utilizing the TruSeq Library Prep Kit 2.0 per the manufacturers specifications. . Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries.

tag: donor id

value: Donor #1

value: human cord-blood endothelial cells

tag: genotype/variation

value: CRISPR/Cas9 CIITA

tag: passage

value: Human IFN-y (50ng/mL) x 72h


title: CIITA-null, Donor 2, Clone 1 [CIITA_Donor2_Rep3]

value: Donor #2


title: Sample_67392: HFD-DR24wk

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then processed using the Hisat2 sequence analysis programs. Reads were mapped to the NCBI reference mouse transcriptome (NCBI GRCm 38) to identify transcripts.
Count value were calculated by featureCount
Normalized by DESeq2 with rlogTransformed
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include rlogTransformed values for each Sample ...

source_name: sciatic nerve

extract_protocol:
Tissues [sciatic nerve (SCN, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS‐122‐2001, RS‐122‐2002; Illumina, San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: sciatic nerve

value: 24 weeks

tag: diet

value: HFD

tag: stz-treatment

value: Without STZ

tag: dietary reversal

value: DR


title: Sample_67423: HFD-DR24wk

tag: age


title: Sample_67376: HFD-DR24wk


title: Rictorfl/fl LysM+/cre Colon_Macrophages_#4

city: Vienna

first: Thomas

last: Weichhart

address: Waehringerstraße 10

department: Center for Pathobiochemistry and Genetics

institute: Medical University of Vienna

hyb_protocol: Samples were hybridized with Affymetrix GeneChip® Mouse Gene 2.0 ST arrays

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Normalization of the data was done with the Affymetrix Expression Console. Analysis was performed with the Affymetrix Transcriptome Analysis Console (TAC) v3.0. We considered genes to be differentially regulated between Rictorfl/fl LysM+/+ and Rictorfl/fl LysM+/cre Colon macropahges that were more than two-fold differently expressed with a ANOVA significance value of smaller than 0.05.

source_name: Rictorfl/fl LysM+/cre mouse

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: In order to induce colitis, mice were treated with 5%DSS for 5 days, followed by 3 days of normal water. Colon of the mice was digested and macrophages were sorted from the lamina propria cells. Macrophages were defined as being CD45+ CD11b+ CD64+ MHCII+ Ly6C-.

extract_protocol: Colon macrophages were taken up in Trizol and RNA was isolated by phenol-chloroform extraction, followed by Quiagen Rneasy Plus Micro Kit according to the manufacturers instructions.

treatment_protocol: Mice were treated with 5%DSS for 5 days. After another 3 days of normal water, colon was isolated and macrophages were isolated.

value: Colon

value: Macrophage

value: Rictorfl/fl LysM+/cre


title: CIITA-null, Donor 2, Clone 12 [CIITA_Donor2_Rep2]

tag: treatment


title: Sample_67344: HFD-DR24wk


title: Sample_67408: HFD-DR24wk


title: DOX- 3

city: Gifu

first: Hiroyuki

last: Tomita

address: 1-1 Yanagido

institute: Gifu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: epithelia of CBD, NO-treated iFGF10  mouse

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using RNAeasy mini kit (Quiagen) according to the manufacturer's instructions.

treatment_protocol: DOX+: Doxycycline 0.02% in Water  free drinkig 5 days, DOX-: Water only, free drinking 5 days

tag: agent

value: water

tag: strain

value: Epithelia of CBD(common bile duct)


title: DOX- 2

tag: tissue


title: DOX+1

source_name: epithelia of CBD, DOX-treated iFGF10  mouse

value: Doxycycline


title: Rictorfl/fl LysM+/+ Colon_Macrophages_#2

source_name: Rictorfl/fl LysM+/+ mouse

value: Rictorfl/fl LysM+/+


title: B2M-null+CIITA-null, Donor 1, Clone 8 [B2M_CIITA_Donor1_Rep3]

source_name: CRISPR/Cas9 B2M+CIITA targeted Human cord-blood endothelial cells

value: Donor #1

value: CRISPR/Cas9 B2M+CIITA


title: Rictorfl/fl LysM+/+ Colon_Macrophages_#3


title: DOX- 1


title: DOX+2


title: Sample_67440: HFD-DR24wk


title: CIITA-null, Donor 1, Clone 8 [CIITA_Donor1_Rep3]

value: human cord-blood endothelial cells

value: CRISPR/Cas9 CIITA


title: DOX+3


title: B2M-null+CIITA-null, Donor 2, Clone 2 [B2M_CIITA_Donor2_Rep3]

value: Donor #2

value: Human IFN-y (50ng/mL) x 72h


title: Sample_67442: HFD-STZ-DR24wk

value: sciatic nerve

value: 24 weeks

value: With STZ


title: Sample_67425: HFD-STZ-DR24wk

value: HFD

value: DR


title: Abl B Bim3’UTRmut/mut 10

first: Verena

last: Labi

institute: Medical University Innsbruck

description:
miRNA
SAMPLE 10

tag: developmental stage

value: embryo

tag: strain (genetic background)

value: liver

value: Abelson virus transformed B cell progenitors


title: B2M-null+CIITA-null, Donor 1, Clone 10 [B2M_CIITA_Donor1_Rep2]

tag: cell type


title: Rictorfl/fl LysM+/+ Colon_Macrophages_#1

value: Colon

value: Macrophage


title: Sample_67410: HFD-STZ-DR24wk


title: Rictorfl/fl LysM+/cre Colon_Macrophages_#2

value: Rictorfl/fl LysM+/cre


title: B2M-null+CIITA-null, Donor 2, Clone 12 [B2M_CIITA_Donor2_Rep2]


title: Healthy control biological rep4

city: Chicago

first: Justin

middle: Eze

last: Ideozu

state: IL

address: 255 E Chicago Avenue

department: Human Molecular Genetics

institute: Lurie Children's Hospital

description:
Differential miRNA expression between cystic fibrosis versus non-Cystic fibrosis samples
HC4

hyb_protocol: Hybridization was performed by injecting the labelled samples, which were mixed with hybridization cocktail (130 μL total volume), into the 100 Format miRNA microarrays and subsequent incubation in a 48ºC hybridization oven with continuous agitation at 60 rpm for 16 hrs.

scan_protocol: Scanning was performed using the Affymetrix Genechip 3000 Scanner

data_processing: Data were accessed for quality using Transcriptome Analysis Console software (v.4.0.1) and normalized with RMA.

source_name: Plasma

label_protocol: Using the Affymetrix GeneChip miRNA 4.0 array, 8ul of plasma from each sample was labelled using FlashTag Biotin RNA Labelling kit

extract_protocol: Frozen samples; Mixture with Trizol Reagent followed by extraction with RNA Clean and Concentrator kit

value: Plasma

tag: diagnosis

value: Non Cystic fibrosis


title: Healthy control biological rep5

description:
Differential miRNA expression between cystic fibrosis versus non-Cystic fibrosis samples
HC5


title: Sample_67394: HFD-STZ-DR24wk


title: Healthy control biological rep3

description:
Differential miRNA expression between cystic fibrosis versus non-Cystic fibrosis samples
HC3


title: Healthy control biological rep2

description:
Differential miRNA expression between cystic fibrosis versus non-Cystic fibrosis samples
HC2


title: Cystic fibrosis, biological rep5

description:
Differential miRNA expression between cystic fibrosis versus non-Cystic fibrosis samples
CF5

value: Cystic fibrosis


title: Cystic fibrosis, biological rep3

description:
Differential miRNA expression between cystic fibrosis versus non-Cystic fibrosis samples
CF3


title: Sample_67362: HFD-STZ-DR24wk


title: Sample_67346: HFD-STZ-DR24wk


title: B2M-null+CIITA-null, Donor 1, Clone 10 [B2M_CIITA_Donor1_Rep1]

value: Donor #1

value: human cord-blood endothelial cells

value: CRISPR/Cas9 B2M+CIITA


title: B2M-null+CIITA-null, Donor 2, Clone 11 [B2M_CIITA_Donor2_Rep1]

value: Donor #2

value: Human IFN-y (50ng/mL) x 72h


title: Cystic fibrosis, biological rep4

description:
Differential miRNA expression between cystic fibrosis versus non-Cystic fibrosis samples
CF4


title: B2M-null, Donor 2, Clone 9 [B2M_Donor2_Rep3]

source_name: CRISPR/Cas9 B2M targeted Human cord-blood endothelial cells

value: CRISPR/Cas9 B2M


title: Cystic fibrosis, biological rep2

description:
Differential miRNA expression between cystic fibrosis versus non-Cystic fibrosis samples
CF2


title: Cystic fibrosis, biological rep1

description:
Differential miRNA expression between cystic fibrosis versus non-Cystic fibrosis samples
CF1


title: Sample_67406: HFD-STZ16wk

value: sciatic nerve

value: 16 weeks

value: HFD

value: With STZ


title: B2M-null, Donor 1, Clone 7 [B2M_Donor1_Rep3]


title: Healthy control biological rep1

description:
Differential miRNA expression between cystic fibrosis versus non-Cystic fibrosis samples
HC1


title: Sample_67390: HFD-STZ16wk


title: CIITA-null, Donor 1, Clone 7 [CIITA_Donor1_Rep2]

value: CRISPR/Cas9 CIITA


title: Sample_67360: HFD-DR24wk

value: 24 weeks

value: Without STZ

value: DR


title: Sample_67374: HFD-STZ16wk


title: B2M-null, Donor 1, Clone 4 [B2M_Donor1_Rep2]


title: Sample_67358: HFD-STZ16wk


title: ONC-S2

first: Linqing

last: Miao

address: No.5 Zhongguancun South St, Haidian District

department: Advanced Innovation Center

institute: Beijing Institute of Technology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.0.5
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010. In short, FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene,
Genome_build: mm10
Supplementary_files_format_and_content: excel files include gene counts and FPKM values for each Sample

source_name: Retina

extract_protocol:
Retinas were removed and RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: retina

value: 5 weeks

tag: genotype

value: wild type

value: optic nerve crush injury with GV16 treatment


title: ONC-J3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.0.5
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010. In short, FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene,
Genome_build: mm10
Supplementary_files_format_and_content: Files include gene counts and FPKM values for each Sample

value: optic nerve crush injury with BL1 treatment


title: B2M-null, Donor 2, Clone 6 [B2M_Donor2_Rep2]

value: human cord-blood endothelial cells


title: ONC-S1


title: B2M-null, Donor 1, Clone 3 [B2M_Donor1_Rep1]

value: Donor #1


title: ONC-J1


title: Sample_67342: HFD-STZ16wk


title: B2M-null, Donor 2, Clone 3 [B2M_Donor2_Rep1]

value: Donor #2

value: Human IFN-y (50ng/mL) x 72h


title: ONC-F1

value: optic nerve crush injury with GB20 treatment


title: ONC3

value: optic nerve crush injury


title: Sample_67452: HFD-STZ24wk

value: sciatic nerve

value: HFD


title: Rictorfl/fl LysM+/cre Colon_Macrophages_#1

value: Colon

value: Macrophage

value: Rictorfl/fl LysM+/cre


title: ONC2


title: Sample_67441: HFD-STZ24wk

value: 24 weeks

value: With STZ


title: ONC-S3

value: retina

value: 5 weeks


title: ONC1

value: wild type


title: Control, Donor 2, Clone 4 [AAVS1_Donor2_Rep3]

source_name: CRISPR/Cas9 AAVS1 targeted Human cord-blood endothelial cells

value: CRISPR/Cas9 AAVS1


title: Sample_67424: HFD-STZ24wk


title: Sample_67409: HFD-STZ24wk


title: ONC-J2

value: optic nerve crush injury with BL1 treatment


title: Control, Donor 2, Clone 3 [AAVS1_Donor2_Rep2]

value: human cord-blood endothelial cells


title: Control, Donor 1, Clone 2 [AAVS1_Donor1_Rep2]

value: Donor #1


title: Rictorfl/fl LysM+/cre Colon_Macrophages_#3


title: ONC-F2


title: WT2

value: naïve control


title: Control, Donor 1, Clone 8 [AAVS1_Donor1_Rep3]

value: Human IFN-y (50ng/mL) x 72h


title: WT1


title: ONC-F3

value: optic nerve crush injury with GB20 treatment


title: Sample_67393: HFD-STZ24wk

value: sciatic nerve


title: Sample_67377: HFD-STZ24wk

value: HFD


title: Control, Donor 1, Clone 11 [AAVS1_Donor1_Rep1]


title: Control, Donor 2, Clone 2 [AAVS1_Donor2_Rep1]

value: Donor #2


title: Sample_67361: HFD-STZ24wk


title: WT3


title: TNF3a_1

city: Izmir

first: ipek

last: erdogan

address: Gulbahce

country: Turkey

institute: Izmir Institute of Technology

data_processing:
The original raw data from high throughput sequencing (Illumina HiSeqTM2500) which consisted of raw pictures were first transformed to Sequenced Reads which contained reads sequence and corresponding base quality(in FASTQ format) through Base Calling
Base calling errors were predicted by Illumina Casava 1.8 and related to Phred quality scores Q
Novel circRNAs were identified and annotated by CIRCexplorer (Xiao-Ou Zhang et al., 2014), which remap the unmapped reads to the genome by tophat's fusion-search to find back-spliced reads. The junction reads that have more than 2 support reads are annotated as novel circRNAs, and those mapped to introns and exons are annotated as ciRNAs and circRNAs, respectively.
The normalized expression of circRNAs in each sample are calculated based on the TPM (Zhou et al., 2010) method. For samples with biological replicates, DESeq2 (Michael et al., 2014) was used to do the differential expression analysis and filtration threshold was normally set as padj < 0.05.
Source genes of differential circRNAs were analyzed by Gene Ontology and KEGG pathway. To further study the functions of circRNAs, the pairing of circRNAs and miRNAs are annotated by miRanda
Genome_build: GRCh38.82
Supplementary_files_format_and_content: Readcounts and TPMs

source_name: HeLa cells

growth_protocol: HeLa cells were routinely cultured in RPMI medium supplemented with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
Total RNAs were extracted by Trizol
RNA libraries were prepared using HiSeq high-throughput sequencing by sequencing by synthesis

treatment_protocol: Hela cells were treated with 80 µM cisplatin for 16h, 0.5 µM doxorubicin for 4h, 125 ng/µl TNF-alpha supplemented with 10 µg/ml cycloheximide for 8h, 5 µg/ml anti-Fas mAb for 16h and 0.1% DMSO for 16h.

tag: cell line

value: HeLa

value: cervix epithelial

tag: passages

value: TNF-alpha


title: Sample_67345: HFD-STZ24wk

value: 24 weeks

value: With STZ


title: TNF2a_1


title: Sample_67438: HFD16wk

value: 16 weeks

value: Without STZ


title: siTut47-2C-rep3

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
RNA-Seq was performed with biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1. Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1. Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments) and was further normalized with the ERCC spike-in. Samples prepared in different batches were normalized by the 1Cell-stage embryo sample in each batch.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples

source_name: siTut4/7 Mouse 2Cell embryo

growth_protocol: The embyos are clutured in KSOM in vitro

extract_protocol:
Embryos were collected from indicated genotypes (10 embryos per sample). Each sample was directly lysed with 4.2 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 1:1000 ERCC spike-in) and immediately used for cDNA synthesis using the Smart-seq2 method as described previously (Picelli et al, 2014).
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads

treatment_protocol: Zygotic Tut4/7 transcript deletion by small-interfering-RNA (siRNA) microinjection into mouse zygotes.


title: WT-1C-rep3

source_name: Mouse 1Cell embryo


title: WT-2C-rep3

source_name: Mouse 2Cell embryo


title: F81_BLSA2_CD4_O [CD4_O_replicate23]

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina's HumanHT-12 V4.0 Expression Bead Chips (Illumina, San Diego, CA). Each BeadChip has more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.54 μm using the Illumina iScan scanner.

data_processing:
Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores is supplied.
Detection_Pval = Detection Pvalue from Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0.

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5 μg of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

growth_protocol: Samples were derived either from BLSA participants or normal donors. Participants enrolled in the BLSA (NIA protocol #03-AG-0325) are volunteers who at the time of study enrollment were “healthy” based on strict eligibility criteria. BLSA participants tend to be healthier than the general population. Young normal donors are volunteers who have donated blood through the Tissue Procurement for Biomedical Research protocol (NIA protocol #03-AG-N322) or apheresis material through the Cytapheresis of Volunteer Donors protocol (NIA protocol #03-AG-N316). All individuals were consented for their donations and protocols have been reviewed by the appropriate institutional review board at NIH. Total CD4+ T cells were isolated from apheresis-derived peripheral blood mononuclear cells (PBMCs) from 33 donors divided into a younger group (5 men and 3 women, ages 25-38 years old) and an older group (19 men and 6 women, ages 70-82 years old participants in  the BLSA.

extract_protocol: Cell pellets were lysed in 350 μL RLT buffer (QIAGEN Inc, Valencia, CA, USA), and total RNA  extracted from frozen cell pellets containing 5x106 cells using the Qiagen RNeasy Mini Kit (QIAGEN Inc, Valencia, CA, USA) according to the manufacturer’s instructions. RNA quantity and integrity was evaluated by Nanodrop and Agilent Bioanalyzer RNA 6000 Chip (Agilent, Santa Clara, CA).

treatment_protocol: PBMCs were isolated from apheresis packs using Ficoll-Paque Plus (GE Healthcare, Piscataway, NJ, USA) density gradient. CD4+ T cells were obtained by positive selection using anti-human CD4 microbeads (Miltenyi Biotec Auburn, CA, USA) (29). CD4+ T cells in RPMI 1640+1% P/S/G+10% FBS medium were incubated for 4h at 37ºC (5% CO2 incubator) CD4+ T cells were then washed and collected by centrifugation.

tag: subject status

value: healthy participants of the Baltimore Longitudinal Study on Aging (BLSA)

tag: Sex

value: F

value: CD4+ T cells


title: M82_BLSA54_CD4_O [CD4_O_replicate24]

value: M


title: M79_BLSA39_CD4_O [CD4_O_replicate21]


title: F80_BLSA40_CD4_O [CD4_O_replicate22]


title: M82_BLSA82_CD4_O [CD4_O_replicate25]


title: TNF1a_1


title: siTut47-2C-rep1

tag: stain

value: 2 cell embryo

tag: genotype/variation


title: M75_BLSA63_CD4_O [CD4_O_replicate20]


title: FAS3a_1

value: anti-Fas mAb


title: Sample_67405: HFD16wk

tag: diet

tag: stz-treatment

tag: dietary reversal


title: FAS2a_1

tag: treatment


title: Sample_67437: HFD16wk

tag: age


title: Sample_67389: HFD16wk

tag: tissue


title: WT-2C-rep2

value: wild type


title: Sample_67373: HFD16wk

value: sciatic nerve


title: CIITA-null, Donor 2, Clone 11 [CIITA_Donor2_Rep1]

tag: donor id

value: human cord-blood endothelial cells

value: CRISPR/Cas9 CIITA

tag: passage

value: Human IFN-y (50ng/mL) x 72h


title: FAS1a_1

value: HeLa

tag: cell type

value: cervix epithelial


title: DOX3a_1

value: doxorubicin


title: WT-1C-rep2

value: 1 cell embryo


title: WT-2C-rep1


title: WT-1C-rep1


title: siTut47-2C-rep2


title: Sample_67357: HFD16wk

value: 16 weeks

value: HFD


title: P301S-TIA1_het_1

city: Rochester

first: Hu

last: Li

address: 200 First Street, Gonda Building G19-408

institute: Mayo Clinic

data_processing:
alignment TopHat v2.0.6
featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited gene raw counts

extract_protocol:
Total brain (cortex) RNA extracts were purified according to manufacturer’s instruction using the Qiagen Qiazol Lysis Reagent (Cat# 79306) and RNeasy Mini kit (Cat# 73404).
Paired-end sequencing libraries were prepared by the Mayo Clinic sequencing core facilities (Rochester, MN) with the TruSeq Stranded Total Sample Preparation kit (Illumina), after which samples were subjected to quality control, cluster generation, and sequencing at a read depth of 60 million reads per sample on the Illumina HiSeq 2000 platform.

value: TIA1 heterogeneous mouse

value: 9 months

tag: brain

value: brain


title: M75_BLSA9_CD4_O [CD4_O_replicate19]

value: healthy participants of the Baltimore Longitudinal Study on Aging (BLSA)

value: M

value: CD4+ T cells


title: F75_BLSA13_CD4_O [CD4_O_replicate18]

value: F


title: M74_BLSA36_CD4_O [CD4_O_replicate16]


title: M74_BLSA46_CD4_O [CD4_O_replicate17]


title: DOX2a_1


title: DOX1a_1


title: Sample_67453: HFD24wk

value: sciatic nerve

value: 24 weeks

value: Without STZ


title: RRBS-RPC-3

city: Guangzhou

first: Shuyi

last: Chen

address: #7 Jinsui Rd, Zhujiang Newtown

institute: Zhongshan Ophthlamic Center

data_processing:
RNA-seq: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15 b) 13% base quality <20.
RNA-seq: Hisat2 2.0.4 mapping to reference genome.
RNA-seq: Count counting.
RRBS: We applied quality and adapter trimming to FastQ files with the Perl Programm Trim Galore (version 0.4.3).
RRBS: Bismark v0.16.3 mapping to reference genome.
RRBS: Differential methylation analysis was performed using methylKit (Version 1.4.0).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RNA-seq: TXT file contains counts for each sample.
Supplementary_files_format_and_content: RRBS: TXT files contain differential methylation results.

source_name: Retinal progenitor cells

extract_protocol:
Mouse Müller cells were FACS sorted from Rlbp1-GFP reporter mice (2-3-month-old young mice, 1.5-year-old aged mice, and 2-3-month-old young mice treated with intravitrea NMDA injection two days before sample collection). Retinal progenitor cells (RPCs) were collected from embryonic day 12.5 mouse embryos. Cells were collected and stored in Trizol reagent. Genomic DNAs were extracted with Genomic DNA purification Kit from Promega.
RNA-Seq libraries were constructed using standard Illumina library construction protocol.
Standard RRBS method was used to construct DNA methylome library.

tag: strain/background

value: embryonic day 12.5

value: Retina

value: Retinal progenitor cells


title: CP1a_1

tag: cell line

value: HeLa

value: cervix epithelial

value: cisplatin


title: Sample_67426: HFD24wk

value: HFD


title: Sample_67411: HFD24wk


title: RRBS-RPC-1


title: RRBS-Mü-Aged-3

source_name: Müller cells

value: 1.5 year

value: Muller cells


title: RRBS-Mü-Aged-2


title: RRBS-Mü-Aged-1


title: Sample_67395: HFD24wk


title: Sample_67443: HFD24wk


title: Sample_67341: HFD16wk

value: 16 weeks


title: M73_BLSA7_CD4_O [CD4_O_replicate14]

value: healthy participants of the Baltimore Longitudinal Study on Aging (BLSA)


title: M73_BLSA26_CD4_O [CD4_O_replicate15]

value: M


title: M72_BLSA22_CD4_O [CD4_O_replicate10]

value: CD4+ T cells


title: F73_BLSA50_CD4_O [CD4_O_replicate13]

value: F


title: M72_BLSA56_CD4_O [CD4_O_replicate12]


title: RRBS-RPC-2


title: RRBS-Mü-NMDA-3

value: 2-3 months

value: NMDA


title: C2a_1

tag: passages

value: DMSO


title: M72_BLSA42_CD4_O [CD4_O_replicate11]

tag: subject status


title: Sample_67379: HFD24wk

value: sciatic nerve

value: 24 weeks

value: Without STZ


title: C3a_1

value: HeLa


title: CP2a_1

value: cervix epithelial


title: Sample_67363: HFD24wk


title: C1a_1


title: RRBS-Mü-NMDA-2

value: Retina


title: Prostate: HMN_PC_061(-)

city: Paris

first: Marina

last: Pinskaya

address: 26 rue d'Ulm

institute: Institut Curie

description: total ribo-depleted RNA

data_processing:
Reads were mapped with tophat version 2.0.6, with the following parameters : -N 3 --read-edit-dist 3 -r 155 --mate-std-dev 80 –no-coverage-search --library-type fr-firststrand.
Only unique mapped reads were kept for further analysis.
Read counting was performed using featureCounts version 1.6.0, for the alignment file of each sample, on the annotation gencode27lift37 (using the “gene_id”) and on the new discovered contigs (both annotations put in the same file in SAF-format, as described by the requirements of the program), with the following parameters : -F "SAF" -p -s 2 -O.
Differential expression analysis was performed using Deseq2 version 1.18.1, with default options (genes with 0 count in all samples were preliminarily removed, then a pseudocount of “1” was added).
Genome_build: hg19
Supplementary_files_format_and_content: For each sample, tab-delimited text file of raw counts (the first column is the gene ID, and the second column is the raw count value)

source_name: prostate

growth_protocol: Tumor and normal biopsy specimens were obtained from prostate cancer patients who provided informed consent and were approved for collection and distribution by Mondor institutional board.

extract_protocol:
Total RNA was extracted using Trizol, according to manufacturer’s procedure, quantified and quality controlled using a 2100 Bioanalyzer (Agilent). RNA samples with RNA Integrity Number (RIN) above 6 were depleted for ribosomal RNA and converted into cDNA library using a TruSeq Stranded Total Library Preparation kit (Illumina). cDNA libraries were normalized using an Illumina Duplex-specific Nuclease (DSN) protocol prior to a paired-end sequencing on HiSeq™ 2500 (Illumina).
Total RNA-seq libraries were prepared with TruSeq Stranded Total RNA Sample Prep Kit (RS-122-2201, Illumina)

value: normal prostate

tag: gleason score(prostatoctomy)

tag: tnm score


title: Sample_67436: SD16wk

source_name: sciatic nerve

value: SD


title: Prostate: HMN_PC_086(-)

description: total ribo-depleted RNA


title: RRBS-Mü-3

value: Muller cells


title: RRBS-Mü-NMDA-1


title: Prostate: HMN_PC_202(-)

description: total ribo-depleted RNA


title: Sample_67404: SD16wk

value: 16 weeks


title: Sample_67388: SD16wk


title: RRBS-Mü-2


title: Prostate: HMN_PC_149(-)

description: total ribo-depleted RNA


title: Prostate: HMN_PC_132(-)

description: total ribo-depleted RNA


title: Sample_67372: SD16wk


title: Sample_67340: SD16wk


title: F71_ND31_CD4_O [CD4_O_replicate6]

value: healthy participants of the Baltimore Longitudinal Study on Aging (BLSA)

tag: Sex


title: RNA-RPC-2

description: processed data file: all.counts.txt

value: embryonic day 12.5

value: Retinal progenitor cells


title: M71_BLSA31_CD4_O [CD4_O_replicate8]

value: M

value: CD4+ T cells


title: Prostate: HMN_PC_125(-)

description: total ribo-depleted RNA


title: Prostate: HMN_PC_093(-)

description: total ribo-depleted RNA


title: Sample_67451: SD24wk

tag: diet


title: RNA-RPC-1

description: processed data file: all.counts.txt


title: Prostate: HMN_PC_78(-)

description: total ribo-depleted RNA


title: Sample_67422: SD24wk

tag: stz-treatment


title: RNA-Mü-Aged-2

description: processed data file: all.counts.txt

value: 1.5 year


title: M71_BLSA43_CD4_O [CD4_O_replicate9]


title: M70_BLSA57_CD4_O [CD4_O_replicate4]


title: M70_BLSA83_CD4_O [CD4_O_replicate5]


title: RRBS-Mü-1

value: 2-3 months


title: RNA-RPC-3

description: processed data file: all.counts.txt


title: M71_BLSA23_CD4_O [CD4_O_replicate7]


title: M70_BLSA17_CD4_O [CD4_O_replicate2]


title: M70_BLSA48_CD4_O [CD4_O_replicate3]


title: F38_BLSA71_CD4_Y [CD4_Y_replicate8]

value: F


title: F70_BLSA47_CD4_O [CD4_O_replicate1]


title: M33_ND554_CD4_Y [CD4_Y_replicate7]


title: Prostate: HMN_PC_130

description: total ribo-depleted RNA

value: prostate tumor


title: RNA-Mü-Aged-1

description: processed data file: all.counts.txt


title: Prostate: HMN_PC_148

description: total ribo-depleted RNA


title: Sample_67407: SD24wk

value: sciatic nerve

value: 24 weeks

value: Without STZ

tag: dietary reversal


title: RNA-Mü-NMDA-3

description: processed data file: all.counts.txt

value: Retina

tag: treatment

value: NMDA


title: Sample_67391: SD24wk

tag: age

value: SD


title: M32_ND691_CD4_Y [CD4_Y_replicate6]


title: RNA-Mü-NMDA-2

description: processed data file: all.counts.txt

tag: tissue

value: Muller cells


title: Prostate: HMN_PC_121

description: total ribo-depleted RNA


title: Prostate: HMN_PC_009

description: total ribo-depleted RNA


title: Sample_67375: SD24wk


title: Sample_67439: SD24wk


title: Prostate: HMN_PC_085

description: total ribo-depleted RNA


title: RNA-Mü-NMDA-1

description: processed data file: all.counts.txt


title: RNA-Mü-2

description: processed data file: all.counts.txt


title: M30_ND340_CD4_Y [CD4_Y_replicate5]


title: Prostate: HMN_PC_033

description: total ribo-depleted RNA


title: Sample_67343: SD24wk


title: Sample_67359: SD24wk


title: RNA-Mü-1

description: processed data file: all.counts.txt


title: 24303_M3_E2_Plus_PBDE

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline  to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using CellRanger's default settings
Genome_build: mm10
Supplementary_files_format_and_content: text files containing the raw gene expression count

source_name: Mammary gland

extract_protocol:
Mammary glands were digested using a mixture of Collagenase and DNAseI, and processed into a single-cell suspension for loading onto a Chromium Controller (10x Genomics).
Cell number and viability were measured using a TC20 Automated Cell Counter (BioRad). Single-cell RNA libraries were prepared according to the Chromium™ Single Cell 3' Reagent Kits v2 User Guide (10x Genomics). Approximately 4,000 cells were loaded on a Chromium single cell Controller instrument (10x Genomics) to generate single cell gel beads in emulsion (GEMs). The barcoded sequencing libraries were constructed using the Chromium Single-Cell 3′ Library Kit (10x Genomics) for enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, ligation cleanup, sample index PCR, and PCR cleanup.

treatment_protocol: Mice were exposed to regular diet without PBDE, E2 (1ug/injection daily), or E2 + PBDE (BDE-47 = 1mg/kg bw/day, BDE-100 = 0.056 mg/kg bw/day, and BDE-153 = 0.126 mg/kg bw/day).

value: Mammary gland

tag: strain

value: BALB/cj

value: 9 weeks

tag: gender

value: female


title: CP3a_1

value: HeLa

tag: cell type

value: cervix epithelial

value: cisplatin


title: Prostate: HMN_PC_139

description: total ribo-depleted RNA


title: Adipocytes cocultured rep3

city: Shanghai

first: Zhiwei

last: Cai

state: Shanghai

address: Yan'an Road 221

department: Department of Surgery

institute: Huadong Hospital of Fudan University

data_processing:
The raw reads were trimmed and quality controlled by SeqPrep  and Sickle  with default parameters.
The clean reads were separately aligned to reference genome with orientation mode using bowtie2 software
The expression level for each gene was calculated using the fragments per kilobase of transcript per millions base pairs sequenced (FPKM) method
Genome_build: mm10

growth_protocol: The 3T3-L1 preadipocytes were cultured in DMEM with 10% newborn calf serum. Two days after 100% of conﬂuence (designated Day 0), 3T3-L1 preadipocytes were induced to differentiate in DMEM containing 10% FBS, 0.5 mM 3-isobutyl-1-methylxanthine (M), 1 μM dexamethasone (D), 1 μg/ml insulin (I) for 2 days. After 48h (Day 2), these cells were sustained in DMEM with 10% FBS and 1 ug/ml insulin for another 2 days. Then, 3T3-L1 mature adipocytes were cultured in DMEM with 10% FBS.

extract_protocol:
Total RNA was extracted from 3T3-L1 mature adipocytes using TRIzol reagent. Genomic DNA was removed using DNase I.
The RNA-seq libraries were prepared according to TruSeqTM RNA sample preparation Kit from Illumina

value: co-cultured with Panc-1

value: fibroblast


title: Prostate: HMN_PC_195

description: total ribo-depleted RNA

value: prostate tumor


title: M30_BLSA10_CD4_Y [CD4_Y_replicate4]

value: healthy participants of the Baltimore Longitudinal Study on Aging (BLSA)

value: M

value: CD4+ T cells


title: F29_ND60A_CD4_Y [CD4_Y_replicate3]

value: F


title: Adipocytes cocultured rep2


title: 24306_M3_Vehicle

value: Vehicle


title: Prostate: HMN_PC_131

description: total ribo-depleted RNA


title: Prostate: HMN_PC_124

description: total ribo-depleted RNA


title: Adipocytes cocultured rep1


title: 23789_M4_E2


title: thyroid_normal [PTMC8 matched normal]

city: Seoul

first: Sohee

last: Lee

address: 222 BANPO-DAERO, SEOCHO-GU

department: Surgery

country: South Korea

institute: The Catholic University of Korea

description:
matched normal tissue of sample15
28_2.AVG_Signal

hyb_protocol: Illumina HumanHT-12 v4.0 Expression Beadchip is a direct hybridization assay and targets more than 47000 human probes.   After fragmentation, 750 ng of labeled cRNA samples were hybridized to each HumanHT-12 v4.0 Expression Beadchip for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc.; San Diego, CA, USA).

scan_protocol: Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences; Little Chalfont, UK) following the bead-array manual.   Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: We applied a filtering criterion for data analysis, as a higher signal value was required for detection of p-values of < 0.05. Array probes that have detection p≥0.05 (similar to signal-to-noise ratio) in over 50% of the samples were filtered out (25,391 probes).   Selected gene signal values (for 21,927 probes) were transformed by logarithm and normalized by the quantile method.

source_name: normal thyroid

label_protocol: Total RNA was amplified and purified using the TargetAmpTM-Nano Labeling Kit for Illumina® Expression BeadChip® (EPICENTRE; Madison, WI, USA) to yield biotinylated cRNA, according to the manufacturer’s instructions.   Briefly, in the range of 200500 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo (dT) primer. Second-strand cDNA was synthesized, in-vitro transcribed, and labeled with biotin-NTP.   After purification, the cRNA was quantified spectrophotometrically.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies; Carlsbad, CA, USA) and purified using RNeasy columns (Qiagen; Valencia, CA, USA) according to the manufacturers’ protocols.   The RNA samples were quantified, aliquoted, and stored at -80°C until use. Purity and integrity of RNA was evaluated by denaturing gel electrophoresis and absorbance.   Absorbance measurements at 260 nm were used to quantify RNA (ND-1000 Spectrophotometer) (NanoDrop; Wilmington, DE, USA).  The ratio of absorbance at 260 nm to that at 280 and 230 nm was used as an indication of sample purity, and values of 1.72.0 were considered to indicate relatively pure RNA.   Total-RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA, USA) with an RNA Integrity Number value.

treatment_protocol: We obtained matched thyroid tumor and normal tissues from eight papillary thyroid microcaricinoma patients who underwent thyroidectomy.

tag: disease

value: normal thyroid


title: 23735_M4_E2_Plus_PBDE


title: M25_ND29_CD4_Y [CD4_Y_replicate1]


title: F26_ND703_CD4_Y [CD4_Y_replicate2]


title: Adipocytes alone rep2

value: control


title: 24305_M3_E2

value: Mammary gland


title: Prostate: HMN_PC_092

description: total ribo-depleted RNA


title: 23790_M4_Vehicle

value: BALB/cj


title: Prostate: HMN_PC_77

description: total ribo-depleted RNA


title: Prostate: HMN_PC_167

description: total ribo-depleted RNA


title: Adipocytes alone rep3